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Serafini-Fracassini D, Della Mea M, Parrotta L, Faleri C, Cai G, Del Duca S, Aloisi I. AtPng1 knockout mutant of Arabidopsis thaliana shows a juvenile phenotype, morpho-functional changes, altered stress response and cell wall modifications. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:11-21. [PMID: 34325356 DOI: 10.1016/j.plaphy.2021.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/01/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
In order to ascertain the role of plant transglutaminases (TGase) in growth and abiotic stress response, the AtPng1 knock out (KO) line of A. thaliana has been analyzed during plant development and under heat and wound stress. Comparing wild type (WT) and KO lines a 58-kDa band was immunodetected by anti-AtPng1p antibody in the cell wall and chloroplasts only in the WT line. A residual TGase activity, not showing correlation with development nor stress response, was still present in the KO line. The KO line was less developed, with a juvenile phenotype characterized by fewer, smaller and less differentiated cells. Chloroplast TGase activity was insensitive to mutation. Data on stressed plants showed that (i) KO plants under heat stress were more juvenile compared to WT, (ii) different responses between WT and KO lines after wounding took place. TGase activity was not completely absent in the KO line, presenting high activity in the plastidial fraction. In general, the mutation affected A. thaliana growth and development, causing less differentiated cytological and anatomical features.
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Li D, Huang M, Zhuang Z, Ding R, Gu T, Hong L, Zheng E, Li Z, Cai G, Wu Z, Yang J. Genomic Analyses Revealed the Genetic Difference and Potential Selection Genes of Growth Traits in Two Duroc Lines. Front Vet Sci 2021; 8:725367. [PMID: 34557543 PMCID: PMC8453014 DOI: 10.3389/fvets.2021.725367] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/03/2021] [Indexed: 01/02/2023] Open
Abstract
Duroc pigs are famous for their high growth rate, feed conversion efficiency, and lean meat percentage. Given that they have been subjected to artificial selection and breeding in multiple countries, various lines with obvious differences in production performance have formed. In this study, we genotyped 3,770 American Duroc (AD) pigs and 2,098 Canadian Duroc (CD) pigs using the GeneSeek Porcine SNP50 Beadchip to dissect the genetic differences and potential selection genes of growth traits in these two Duroc pig lines. Population structure detection showed that there were significant genetic differences between the two Duroc pig lines. Hence, we performed F ST and cross-population extended haplotype homozygosity (XP-EHH) analyses between the two lines. As a result, we identified 38 annotated genes that were significantly enriched in the gland development pathway in the AD line, and 61 annotated genes that were significantly enriched in the immune-related pathway in the CD line. For three growth traits including backfat thickness (BFT), loin muscle depth (LMD), and loin muscle area (LMA), we then performed selection signature detection at 5 and 10% levels within the line and identified different selected regions and a series of candidate genes that are involved in lipid metabolism and skeletal muscle development or repair, such as IRX3, EBF2, WNT10B, TLR2, PITX3, and SGCD. The differences in selected regions and genes between the two lines may be the cause of the differences in growth traits. Our study suggests significant genetic differences between the AD and CD lines, which provide a theoretical basis for selecting different Duroc lines as sires for different needs.
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Qiao J, Wang S, Zhou J, Tan B, Li Z, Zheng E, Cai G, Wu Z, Hong L, Gu T. ITGB6 inhibits the proliferation of porcine skeletal muscle satellite cells. Cell Biol Int 2021; 46:96-105. [PMID: 34519117 DOI: 10.1002/cbin.11702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/30/2021] [Accepted: 09/12/2021] [Indexed: 01/17/2023]
Abstract
The formation of embryonic muscle fibers determines the amount of postnatal muscles and is regulated by a variety of signaling pathways and transcription factors. Previously, by using chromatin immunoprecipitation-sequencing and RNA-Seq techniques, we identified a large number of genes that are regulated by H3K27me3 in porcine embryonic skeletal muscles. Among these genes, we found that ITGB6 is regulated by H3K27me3. However, its function in muscle development is unknown. In this study, we first verified that ITGB6 was differentially regulated by H3K27me3 and that its expression levels were upregulated in porcine skeletal muscles at embryonic Days 33, 65, and 90. Then, we performed gain- or loss-of-function studies on porcine skeletal muscle satellite cells to study the role of ITGB6 in porcine skeletal muscle development. The proliferation of porcine skeletal muscle satellite cells was studied through real-time polymerase chain reaction, Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine staining, Western blot, and flow cytometry analyses. We found that the ITGB6 gene was regulated by H3K27me3 during muscle development and had an inhibitory effect on the proliferation of porcine skeletal muscle satellite cells.
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Zang X, Gu T, Hu Q, Xu Z, Xie Y, Zhou C, Zheng E, Huang S, Xu Z, Meng F, Cai G, Wu Z, Hong L. Corrigendum: Global Transcriptomic Analyses Reveal Genes Involved in Conceptus Development During the Implantation Stages in Pigs. Front Genet 2021; 12:721458. [PMID: 34422022 PMCID: PMC8376149 DOI: 10.3389/fgene.2021.721458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
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Hong Y, Ye J, Dong L, Li Y, Yan L, Cai G, Liu D, Tan C, Wu Z. Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs. Front Genet 2021; 12:650370. [PMID: 34408768 PMCID: PMC8366400 DOI: 10.3389/fgene.2021.650370] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.
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Yang R, Guo X, Zhu D, Tan C, Bian C, Ren J, Huang Z, Zhao Y, Cai G, Liu D, Wu Z, Wang Y, Li N, Hu X. Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy. Gigascience 2021; 10:giab048. [PMID: 34282453 PMCID: PMC8290195 DOI: 10.1093/gigascience/giab048] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/21/2021] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Uncovering the genetic architecture of economic traits in pigs is important for agricultural breeding. However, high-density haplotype reference panels are unavailable in most agricultural species, limiting accurate genotype imputation in large populations. Moreover, the infinitesimal model of quantitative traits implies that weak association signals tend to be spread across most of the genome, further complicating the genetic analysis. Hence, there is a need to develop new methods for sequencing large cohorts without large reference panels. RESULTS We describe a Tn5-based highly accurate, cost- and time-efficient, low-coverage sequencing method to obtain 11.3 million whole-genome single-nucleotide polymorphisms in 2,869 Duroc boars at a mean depth of 0.73×. On the basis of these single-nucleotide polymorphisms, a genome-wide association study was performed, resulting in 14 quantitative trait loci (QTLs) for 7 of 21 important agricultural traits in pigs. These QTLs harbour genes, such as ABCD4 for total teat number and HMGA1 for back fat thickness, and provided a starting point for further investigation. The inheritance models of the different traits varied greatly. Most follow the minor-polygene model, but this can be attributed to different reasons, such as the shaping of genetic architecture by artificial selection for this population and sufficiently interconnected minor gene regulatory networks. CONCLUSIONS Genome-wide association study results for 21 important agricultural traits identified 14 QTLs/genes and showed their genetic architectures, providing guidance for genetic improvement harnessing genomic features. The Tn5-based low-coverage sequencing method can be applied to large-scale genome studies for any species without a good reference panel and can be used for agricultural breeding.
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Wu J, Ye Y, Quan J, Ding R, Wang X, Zhuang Z, Zhou S, Geng Q, Xu C, Hong L, Xu Z, Zheng E, Cai G, Wu Z, Yang J. Using nontargeted LC-MS metabolomics to identify the Association of Biomarkers in pig feces with feed efficiency. Porcine Health Manag 2021; 7:39. [PMID: 34078468 PMCID: PMC8170940 DOI: 10.1186/s40813-021-00219-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background Improving feed efficiency is economically and environmentally beneficial in the pig industry. A deeper understanding of feed efficiency is essential on many levels for its highly complex nature. The aim of this project is to explore the relationship between fecal metabolites and feed efficiency-related traits, thereby identifying metabolites that may assist in the screening of the feed efficiency of pigs. Results We performed fecal metabolomics analysis on 50 individuals selected from 225 Duroc x (Landrace x Yorkshire) (DLY) commercial pigs, 25 with an extremely high feed efficiency and 25 with an extremely low feed efficiency. A total of 6749 and 5644 m/z features were detected in positive and negative ionization modes by liquid chromatography-mass spectrometry (LC/MS). Regrettably, the PCA could not classify the the samples accurately. To improve the classification, OPLS-DA was introduced. However, the predictive ability of the OPLS-DA model did not perform well. Then, through weighted coexpression network analysis (WGCNA), we found that one module in each positive and negative mode was related to residual feed intake (RFI), and six and three metabolites were further identified. The nine metabolites were found to be involved in multiple metabolic pathways, including lipid metabolism (primary bile acid synthesis, linoleic acid metabolism), vitamin D, glucose metabolism, and others. Then, Lasso regression analysis was used to evaluate the importance of nine metabolites obtained by the annotation process. Conclusions Altogether, this study provides new insights for the subsequent evaluation of commercial pig feed efficiency through small molecule metabolites, but also provide a reference for the development of new feed additives. Supplementary Information The online version contains supplementary material available at 10.1186/s40813-021-00219-w.
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Zhong H, Cheng S, Zhang X, Xu B, Chen J, Jiang X, Hu Y, Cui G, Wei J, Qian W, Huang X, Hou M, Yan F, Wang X, Song Y, Hu J, Liu Y, Ma X, Li F, Wu C, Chen J, Yu L, Bai O, Xu J, Zhu Z, Liu L, Zhou X, Huang L, Tong Y, Niu T, Wu D, Xiong J, Zhang H, Wang C, Ouyang B, Yi H, Cai G, Li B, Liu J, Li Z, Xiao R, Wang L, Jiang Y, Liu Y, Zheng X, Xu P, Huang H, Wang L, Chen S, Zhao W. ESA VERSUS MESA WITH SANDWICHED RADIOTHERAPY IN PATIENTS WITH EARLY‐STAGE NATURAL KILLER/T‐CELL LYMPHOMA: A MULTICENTRE, RANDOMISED, PHASE 3, NON‐INFERIORITY TRIAL. Hematol Oncol 2021. [DOI: 10.1002/hon.52_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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84
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Qiu Y, Ding R, Zhuang Z, Wu J, Yang M, Zhou S, Ye Y, Geng Q, Xu Z, Huang S, Cai G, Wu Z, Yang J. Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs. BMC Genomics 2021; 22:332. [PMID: 33964879 PMCID: PMC8106131 DOI: 10.1186/s12864-021-07654-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
Background In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations. Results Our study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA, GPER1, PNPLA2 and BSCL2. Conclusions The present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07654-7.
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Mo J, Li G, Huang G, Wang H, Shi J, Zhou R, Cai G, Wu Z, Zhang X. Adaptation of Gut Microbiome to Transgenic Pigs Secreting β-Glucanase, Xylanase, and Phytase. Front Genet 2021; 12:631071. [PMID: 33747047 PMCID: PMC7971306 DOI: 10.3389/fgene.2021.631071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022] Open
Abstract
We previously generated transgenic pigs with enhanced growth rate and reduced nutrient loss. However, the composition of their gut microbiome is unknown. In this study, we successfully generated EGFP marker-free transgenic (MF-TG) pigs with high expression levels of microbial β-glucanase, xylanase, and phytase in the parotid gland. We collected intestinal contents from the ileum, cecum and colon of five MF-TG and five wild-type (WT) sows and investigated the gut microbiome of the transgenic pigs via metagenomic analysis. Results showed that the levels of probiotics, such as Lactobacillus reuteri and Streptococcus, were more abundant in the cecum of the MF-TG pigs and higher than those of WT pigs. By contrast, the levels of harmful microorganisms, such as Campylobacter, Chlamydia trachomatis, and Campylobacter fetus, and various unidentified viruses, were higher in the cecum of the WT pigs than those of the MF-TG pigs. By comparing unigenes and the eggNOG database, we found that the microorganisms in the colon of the MF-TG pigs had high fractional abundance in DNA (cytosine-5)-methyltransferase 1 and serine-type D-Ala-D-Ala carboxypeptidase, whereas the aspartate carbamoyltransferase regulatory subunit and outer membrane protein pathways were enriched in the WT pigs. Moreover, the microorganisms in the cecum of the MF-TG pigs were active in GlycosylTransferase Family 8 (GT8), Glycoside Hydrolase Family 13 (GH13), and Glycoside Hydrolase Family 32 (GH32). Furthermore, the levels of numerous carbohydrases, such as glucan 1,3-beta-glucosidase, xylan 1,4-beta-xylosidase and exo-1,3-1,4-glucanase, were higher in the cecum of the MF-TG pigs than those of the WT pigs. The results indicated that intestinal microbes can change adaptively to the secretion of transgenic enzymes, thereby forming a benign cooperation with their host. This cooperation could be beneficial for improving feed efficiency.
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Yang L, Wu X, Zhang N, Shi J, Zhou R, Su Q, Zheng E, Huang S, Xu Z, Hong L, Gu T, Yang J, Yang H, Cai G, Wu Z, Li Z. Knockdown of RLIM inhibits XIST expression and improves developmental competence of cloned male pig embryos. Mol Reprod Dev 2021; 88:228-237. [PMID: 33650239 DOI: 10.1002/mrd.23460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 11/09/2022]
Abstract
Ectopic expression of Xist on the putative active X chromosome is a primary cause of the low developmental efficiency of cloned mouse and pig embryos. Suppression of abnormal Xist expression via gene knockout or RNA interference (RNAi) can significantly enhance the developmental competence of cloned mouse and pig embryos. RLIM is a Xist expression activator, whereas REX1 is an Xist transcription inhibitor, as RLIM triggers Xist expression by mediating the proteasomal degradation of REX1 to induce imprinted and random X chromosome inactivation in mice. This study aimed to test whether the knockdown of RLIM and overexpression of REX1 can repress aberrant Xist expression and improve the developmental ability of cloned male pig embryos. Results showed that injection of anti-RLIM small interfering RNA significantly decreased Xist messenger RNA abundance, increased REX1 protein level, and enhanced the preimplantation development of cloned male porcine embryos. These positive effects were not observed in cloned male pig embryos injected with REX1 expression plasmid, which might be due to the low expression efficiency of injected REX1 plasmid and/or the short half-life of expressed REX1 protein. The findings from this study indicated that RLIM participated in the ectopic activation of Xist expression in cloned pig embryos by targeting REX1 degradation. Furthermore, this study provided a new method to improve cloned pig embryo development by the inhibition of Xist expression via RNAi of RLIM.
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Zang X, Gu T, Hu Q, Xu Z, Xie Y, Zhou C, Zheng E, Huang S, Xu Z, Meng F, Cai G, Wu Z, Hong L. Global Transcriptomic Analyses Reveal Genes Involved in Conceptus Development During the Implantation Stages in Pigs. Front Genet 2021; 12:584995. [PMID: 33719331 PMCID: PMC7943634 DOI: 10.3389/fgene.2021.584995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 02/08/2021] [Indexed: 01/18/2023] Open
Abstract
Prenatal mortality remains a significant concern to the pig farming industry around the world. Spontaneous fetal loss ranging from 20 to 45% by term occur after fertilization, with most of the loss happening during the implantation period. Since the factors regulating the high mortality rates of early conceptus during implantation phases are poorly understood, we sought to analyze the overall gene expression changes during this period, and identify the molecular mechanisms involved in conceptus development. This work employed Illumina's next-generation sequencing (RNA-Seq) and quantitative real-time PCR to analyze differentially expressed genes (DEGs). Soft clustering was subsequently used for the cluster analysis of gene expression. We identified 8236 DEGs in porcine conceptus at day 9, 12, and 15 of pregnancy. Annotation analysis of these genes revealed rRNA processing (GO:0006364), cell adhesion (GO:1904874), and heart development (GO:0007507), as the most significantly enriched biological processes at day 9, 12, and 15 of pregnancy, respectively. In addition, we found various genes, such as T-complex 1, RuvB-like AAA ATPase 2, connective tissue growth factor, integrins, interferon gamma, SLA-1, chemokine ligand 9, PAG-2, transforming growth factor beta receptor 1, and Annexin A2, that play essential roles in conceptus morphological development and implantation in pigs. Furthermore, we investigated the function of PAG-2 in vitro and found that PAG-2 can inhibit trophoblast cell proliferation and migration. Our analysis provides a valuable resource for understanding the mechanisms of conceptus development and implantation in pigs.
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Ruan D, Zhuang Z, Ding R, Qiu Y, Zhou S, Wu J, Xu C, Hong L, Huang S, Zheng E, Cai G, Wu Z, Yang J. Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population. Genes (Basel) 2021; 12:genes12010117. [PMID: 33477978 PMCID: PMC7835741 DOI: 10.3390/genes12010117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.
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Xu C, Wang X, Zhou S, Wu J, Geng Q, Ruan D, Qiu Y, Quan J, Ding R, Cai G, Wu Z, Zheng E, Yang J. Brain Transcriptome Analysis Reveals Potential Transcription Factors and Biological Pathways Associated with Feed Efficiency in Commercial DLY Pigs. DNA Cell Biol 2020; 40:272-282. [PMID: 33297854 DOI: 10.1089/dna.2020.6071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Feed efficiency (FE) is one of the most important economic traits in the porcine industry. In this study, high-throughput RNA sequencing (RNA-seq) was first utilized for brain tissue transcriptome analysis in pigs to indicate the potential genes and biological pathways related to FE in pigs. A total of 8 pigs with either extremely high-FE group (HE-group) or low-FE group (LE-group) were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) between the HE- and LE-group, and 430 DEGs were identified in brain tissues of pigs (|log2(FoldChange)| > 1; adjusted p-values <0.05). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly enriched in synaptic signaling or transmission, and hormone secretion pathways, in which insulin secretion, and oxytocin signaling pathways were closely associated with FE by regulating feeding behavior and energy metabolism (adjusted p-values <0.05). Further, the transcription factors (TFs) analysis and gene co-expression network analysis indicated three hub differentially expressed TFs (NR2F2, TFAP2D, and HNF1B) that affected FE by mainly regulating feeding behavior, insulin sensitivity, or energy metabolism. Our findings suggest several potential TFs and biological pathways for further investigations of FE in pigs.
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Xu Z, Xie Y, Zhou C, Hu Q, Gu T, Yang J, Zheng E, Huang S, Xu Z, Cai G, Liu D, Wu Z, Hong L. Expression Pattern of Seminal Plasma Extracellular Vesicle Small RNAs in Boar Semen. Front Vet Sci 2020; 7:585276. [PMID: 33263017 PMCID: PMC7685987 DOI: 10.3389/fvets.2020.585276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/14/2020] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) regulate multiple physiological processes. Seminal plasma contains numerous EVs that may deliver functional molecules such as small RNAs (sRNAs) to the sperm. However, the RNA profiles in the boar seminal plasma extracellular vesicles (SP-EVs) and its function have not been characterized. The aim of this study was to characterize the functions and sRNA profiles in the boar SP-EVs using deep sequencing technology. Briefly, boar SP-EVs were isolated by differential ultracentrifugation and confirmed with a transmission electron microscope (TEM), nanoparticle tracking analysis (NTA), and Western blot. The isolated boar SP-EVs contained numerous and diverse sRNA families, including microRNAs (miRNAs, 9.45% of the total reads), PIWI-interacting RNAs (piRNAs, 15.25% of the total reads), messenger RNA fragments (mRNA, 25.30% of the total reads), and tRNA-derived small RNAs (tsRNA, 0.01% of the total reads). A total of 288 known miRNAs, 37 novel miRNA, and 19,749 piRNAs were identified in boar SP-EVs. The identified ssc-miR-21-5p may confer negative effects on sperm fertility based on a dual-luciferase reporter experiment. This study therefore provides an effective method to isolate SP-EVs and characterizes the sRNA profile.
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Shi J, Tan B, Luo L, Li Z, Hong L, Yang J, Cai G, Zheng E, Wu Z, Gu T. Assessment of the Growth and Reproductive Performance of Cloned Pietrain Boars. Animals (Basel) 2020; 10:E2053. [PMID: 33171943 PMCID: PMC7694642 DOI: 10.3390/ani10112053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022] Open
Abstract
How to maximize the use of the genetic merits of the high-ranking boars (also called superior ones) is a considerable question in the pig breeding industry, considering the money and time spent on selection. Somatic cell nuclear transfer (SCNT) is one of the potential ways to answer the question, which can be applied to produce clones with genetic resources of superior boar for the production of commercial pigs. For practical application, it is essential to investigate whether the clones and their progeny keep behaving better than the "normal boars", considering that in vitro culture and transfer manipulation would cause a series of harmful effects to the development of clones. In this study, 59,061 cloned embryos were transferred into 250 recipient sows to produce the clones of superior Pietrain boars. The growth performance of 12 clones and 36 non-clones and the semen quality of 19 clones and 28 non-clones were compared. The reproductive performance of 21 clones and 25 non-clones were also tested. Furthermore, we made a comparison in the growth performance between 466 progeny of the clones and 822 progeny of the non-clones. Our results showed that no significant difference in semen quality and reproductive performance was observed between the clones and the non-clones, although the clones grew slower and exhibited smaller body size than the non-clones. The F1 progeny of the clones showed a greater growth rate than the non-clones. Our results demonstrated through the large animal population showed that SCNT manipulation resulted in a low growth rate and small body size, but the clones could normally produce F1 progeny with excellent growth traits to bring more economic benefits. Therefore, SCNT could be effective in enlarging the merit genetics of the superior boars and increasing the economic benefits in pig reproduction and breeding.
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Cai G, Meng X, Yu J. The Predictive Value of Substructure and Whole Heart Dosimetric Variables for Cardiac Events and Overall Survival in Locally Advanced Esophageal Cancer receiving Chemoradiotherapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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93
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Cai G, Meng X, Yu J. A Novel Independent Risk Factor for Radiation Pneumonitis in Lung Cancer Patients Receiving Definitive Radiotherapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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94
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Liu J, Li J, Zeng S, Cai G, Wang Y, Chi J, Li R, Yu Y, Jiao X, Dai Y, Feng Y, Van Zandt M, Seager S, Reich C, Gao Q. Evolution of treatments for endometrial cancers: Clinical data from two national medical databases. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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95
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Cai G, Gao Y, Lu W, Zeng S, Chi J, Jiao X, Li R, Li X, Liu J, Song K, Yu Y, Dai Y, Cui B, Lv W, Kong B, Xie X, Ma D, Gao Q. Ovarian cancer and pretreatment thrombosis-associated indices: Evidence based on multicenter, retrospective, observational study. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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96
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Gao Y, Zeng S, Xiong X, Cai G, Wang Z, Xu X, Chi J, Jiao X, Liu J, Li R, Yao S, Li X, Song K, Tang J, Xing H, Yu Z, Zeng S, Zhang Q, Yi C, Kong B, Xie X, Ma D, Li X, Gao Q. A deep convolutional neural network enabled pelvic ultrasound imaging algorithm for early and accurate diagnosis of ovarian cancer. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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97
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Cai G, Keen HI, Host LV, Aitken D, Laslett LL, Winzenberg T, Wluka AE, Black D, Jones G. Once-yearly zoledronic acid and change in abdominal aortic calcification over 3 years in postmenopausal women with osteoporosis: results from the HORIZON Pivotal Fracture Trial. Osteoporos Int 2020; 31:1741-1747. [PMID: 32361951 DOI: 10.1007/s00198-020-05430-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/22/2020] [Indexed: 12/19/2022]
Abstract
UNLABELLED This study evaluated whether zoledronic acid (ZA) inhibited the progression of abdominal aortic calcification (AAC) over 3 years in 502 postmenopausal women with osteoporosis. AAC progressed in a similar proportion of participants in the ZA (29%) and placebo (31%) groups, suggesting no effect of ZA on AAC progression. INTRODUCTION Bisphosphonate use is associated with reduced risk of all-cause mortality and cardiovascular events. The underlying mechanisms are uncertain but may include effects on vascular calcification. This study aimed to evaluate the effect of zoledronic acid (ZA) on abdominal aortic calcification (AAC) in postmenopausal women with osteoporosis. METHODS This was a post hoc analysis of the HORIZON Pivotal Fracture Trial that included 502 postmenopausal women (mean age 72.5 years) with osteoporosis (234 received ZA and 268 placebo). AAC scores (range, 0-8) were assessed from paired spine X-rays at baseline and after 3 years. Progression of AAC was defined as any increase in AAC score. The association between change in hip and femoral neck bone mineral density and change in AAC score was also assessed. RESULTS At baseline, 292 (58.2%) participants had AAC (i.e., AAC score > 0), with AAC scores similar in the two intervention groups (median [interquartile range], 1 [0 to 2] for both; p = 0.98). Over 3 years, AAC progressed in a similar proportion of participants in both groups (ZA 29% and placebo 31%; p = 0.64). Change in bone mineral density and change in AAC score were not correlated. CONCLUSION Once-yearly zoledronic acid did not affect progression of AAC over 3 years in postmenopausal women with osteoporosis. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT00049829.
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Parrotta L, Aloisi I, Faleri C, Romi M, Del Duca S, Cai G. Chronic heat stress affects the photosynthetic apparatus of Solanum lycopersicum L. cv Micro-Tom. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:463-475. [PMID: 32912485 DOI: 10.1016/j.plaphy.2020.06.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 05/15/2023]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most widely cultivated crops in the world. Tomato is a plant model and the relationship between yield and biotic/abiotic stress has attracted increasing scientific interest. Tomato cultivation under sub-optimal conditions usually negatively impacts growth and development; in particular, heat stress affects several cellular and metabolic processes, such as respiration and photosynthesis. In this work, we studied the effects of chronic heat stress on various cytological and biochemical aspects using the Micro-Tom cultivar as a model. Photosynthetic efficiency decreased during heat stress while levels of post-photosynthetic sugars (sucrose, fructose, glucose and glucose 6-phosphate) oscillated during stress. Similarly, photosynthetic pigments (lutein, chlorophyll a, chlorophyll b and β-carotene) showed an oscillating downward trend with partial recovery during the stress-free phase. The energetic capacity of leaves (e.g. ATP and ADP) was altered, as well as the reactive oxygen species (ROS) profile; the latter increased during stress. Important effects were also found on the accumulation of Rubisco isoforms, which decreased in number. Heat stress also resulted in a decreased accumulation of lipids (oleic and linoleic acid). Photosynthetically alterations were accompanied by cytological changes in leaf structure, particularly in the number of lipid bodies and starch granules. Prolonged heat stress progressively compromised the photosynthetic efficiency of tomato leaves. The present study reports multi-approach information on metabolic and photosynthetic injuries and responses of tomato plants to chronic heat stress, highlighting the plant's ability to adapt to stress.
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Cai G, Cicuttini F, Aitken D, Laslett LL, Zhu Z, Winzenberg T, Jones G. Comparison of radiographic and MRI osteoarthritis definitions and their combination for prediction of tibial cartilage loss, knee symptoms and total knee replacement: a longitudinal study. Osteoarthritis Cartilage 2020; 28:1062-1070. [PMID: 32413465 DOI: 10.1016/j.joca.2020.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To describe the value of radiographic- and magnetic resonance imaging (MRI)-defined tibiofemoral osteoarthritis (ROA and MRI-OA, respectively) and in combination for predicting tibial cartilage loss, knee pain and disability and total knee replacement (TKR) in a population-based cohort. DESIGN A radiograph and 1.5T MRI of the right knee was performed. ROA and MRI-OA at baseline were defined according to the Osteoarthritis Research Society International atlas and a published Delphi exercise, respectively. Tibial cartilage volume was measured over 2.6 and 10.7 years. Knee pain and disability were assessed at baseline, 2.6, 5.1 and 10.7 years. Right-sided TKRs were assessed over 13.5 years. RESULTS Of 574 participants (mean 62 years, 49% female), 8% had ROA alone, 15% had MRI-OA alone, 13% had both ROA and MRI-OA. Having ROA (vs. no ROA) and MRI-OA (vs. no MRI-OA) predicted greater tibial cartilage loss over 2.6 years (-75.9 and -86.4 mm3/year) and higher risk of TKR over 13.5 years (Risk Ratio [RR]: 15.0 and 10.9). Only MRI-OA predicted tibial cartilage loss over 10.7 years (-7.1 mm3/year) and only ROA predicted onset and progression of knee symptoms (RR: 1.32-1.88). In participants with both MRI-OA and ROA, tibial cartilage loss was the greatest (over 2.6 years: -116.1 mm3/year; over 10.7 years: -11.2 mm3/year), and the onset and progression of knee symptoms (RR: 1.75-2.89) and risk of TKR (RR: 50.9) were the highest. CONCLUSIONS The Delphi definition of MRI-OA is not superior to ROA for predicting structural or symptomatic OA progression but, combining MRI-OA and ROA has much stronger predictive validity.
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Antony B, Wang Z, Winzenberg T, Cai G, Laslett L, Aitken D, Hopper I, Singh A, Jones R, Fripp J, Ding C, Jones G. FRI0383 A RANDOMISED PLACEBO-CONTROLLED CLINICAL TRIAL OF CURCUMA LONGA EXTRACT FOR TREATING SYMPTOMS AND EFFUSION-SYNOVITIS OF KNEE OSTEOARTHRITIS (CURKOA TRIAL). Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.5139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Pharmacological therapies are limited, associated with off-target effects, are frequently contraindicated, and only modestly effective for pain in osteoarthritis (OA). Effusion and synovitis are common in OA and are associated with symptomatic and structural progression of OA.Curcuma longa(Turmeric) extract has anti-inflammatory effects and is gaining popularity in the treatment of OA despite the lack of high-quality evidence.Objectives:The CurKOA trial aimed to determine the efficacy ofCurcuma longaextract for reducing knee symptoms and effusion-synovitis in patients with symptomatic knee OA and knee effusion-synovitis.Methods:In this randomised, double-blind, placebo-controlled trial, participants with significant knee pain (≥ 40 mm on a 100-mm visual analog scale [VAS]), symptomatic knee OA (by ACR criteria) and ultrasound defined effusion-synovitis were randomised to receiveCurcuma longaextract (80% aqueous based extract standardized to turmerosaccharides + 20% curcuminoids, 2 × 500 mg capsules/day) or identical placebo for 12 weeks. Knee MRI scans were obtained at baseline and 12 weeks. Coprimary outcomes were changes in knee pain assessed by VAS and change in knee effusion-synovitis volume assessed by MRI over 12 weeks.Results:Among 70 participants (36 receivedCurcuma longa, 34 received placebo, age 61.8±8.6 years, 56% female),Curcuma longasignificantly improved VAS knee pain compared to placebo (-9.11mm, 95% confidence interval [CI] [- 17.79 to -0.44]) over 12 weeks, equivalent to a standardised effect size of 0.50. There was no significant between group difference in change in effusion-synovitis volume (3.24 mL [-0.33, 6.82]). There were significantly greater reductions in WOMAC knee pain (-47.22mm [-81.22, -13.22]), WOMAC function (-112.26mm [-222.79 to -1.74]) and significantly more OARSI-OMERACT treatment responders (63% treatment vs. 38% placebo [Risk Ratio=1.64 (1.00 to 2.70)]) in theCurcuma longagroup compared to the placebo group. There was no significant between-group difference in lateral femoral cartilage T2 relaxation time (-0.38 ms [- 1.10 to 0.34]) assessed from compositional MRI. The incidence of adverse events was similar in theCurcuma longa(n=14 (39%)) and placebo (n=18 (53%)) groups over 12 weeks (P=0.24).Conclusion:An extract ofCurcuma longasignificantly improved knee pain in an inflammatory phenotype of knee OA patients over 12 weeks compared to placebo but had no effect on knee effusion-synovitis and cartilage composition assessed using MRI. The moderate effect size of the treatment supports the use ofCurcuma longaextract for the symptomatic management of knee OA.Figure 1.Change in VAS and WOMAC subscale scores in treatment and control groups over the course of the study. (VAS = Visual analog scale, WOMAC = Western Ontario and McMaster University Index, CL = Curcuma longa extract)Disclosure of Interests:None declared
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